Types of Repetitive Elements

Repetitive elements differ in their position in the genome, sequence, size, number of copies, and presence or absence of coding regions within them. The two major classes of repetitive elements are interspersed elements and tandem arrays.

Interspersed repeated elements are usually present as single copies and distributed widely throughout the genome. The interspersed repeats alone constitute about 45 percent of the genome. The best-characterized interspersed repeats are the transposable genetic elements, also called mobile elements or "jumping genes" (Figure 1).

Repetitive DNA Elements

OOCX,

DISPERSED REPEATS (MOBILE ELEMENTS)

DNA transposons

MITEs (nonautonomous transposon)

LTR Retrotransposons

LTR

Non-LTR retrotransposons (LINEs)

pol II ORF1

ORF2

AAAAA

SINEs (nonautonomous retroposons)

pol III

AAAAA

Retropseudogenes (nonautonomous)

pol III

exon 1

exon 2

exon 3

exon 4

Figure 1. Dispersed repeats are usually found as single units spread throughout the genome. The DNA transposons have two or three open reading frames (ORFs) coding for the factors needed for amplification. LTR retrotransposons are flanked by long terminal repeats (LTR) and have genes such as gag (group antigen gene), and pol (polymerase gene). Non-LTR retrotransposons or LINEs will have ORFs and are transcribed by RNA polymerase II (pol II). There are two nonautonomous repeats thought to parasitize LINEs for its amplification: SINEs and retropseudogenes.

Sequences that are "tandemly arrayed" are present as duplicates, either head to tail or head to head. So-called satellites, minisatellites, and microsatellites largely exist in the form of tandem arrays (these elements originally got their name as "satellites" because they separated from the bulk of nuclear DNA during centrifugation). Sequences repeated in tandem are common at the centromere (where the two halves of a replicated chromosome are held together), and at or near the telomeres (the chromosome tips). Because they are difficult to sequence, sequences repeated in tandem at centromeres and telomeres are underrepresented in the draft sequence of the human genome. This makes it difficult to estimate the copy number, but they certainly represent at least 10 percent of the genome.